10.25386/genetics.6007730.v2
Timthy P. Bilton
Timthy P.
Bilton
John C. McEwan
John
C. McEwan
Shannon M. Clarke
Shannon
M. Clarke
Rudiger Brauning
Rudiger
Brauning
Tracey C. van Stijn
Tracey C.
van Stijn
Suzanne J. Rowe
Suzanne
J. Rowe
Ken G. Dodds
Ken
G. Dodds
Supplemental Material for Bilton et al., 2018
GSA Journals
2018
genotyping-by-sequencing
linkage disequilibrium
maximum likelihood
allelic dropout
low coverage
Genetics
2018-07-13 19:40:31
Dataset
https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Bilton_et_al_2018_in_review_/6007730
Scripts for generating the simulated sequencing data are provided in File S1. Figures S1 and S2 gives bias and standard errors of LD estimates for the second and third simulation scenarios. Figure~S3 gives the standard errors of the allele frequency estimates for all the simulations. Figures S4 and S5 gives the mean square errors of LD estimates for the second and third simulation scenarios. Figure S6 gives the mean read depth distribution for the SNPs used in the deer dataset and Figure S7 gives the distribution of the sequencing error estimates for the deer analysis.